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- PDB-8ho6: ScRIPK WT -

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Basic information

Entry
Database: PDB / ID: 8ho6
TitleScRIPK WT
ComponentsScRIPK kinase protein
KeywordsPLANT PROTEIN / Kinase / RLCK VII
Function / homologyADENOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciesSaccharum hybrid cultivar (sugarcane)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFang, J.L. / Zhang, M.Q.
Funding support2items
OrganizationGrant numberCountry
Other governmentGuikeAA22117007
Other governmentCARS-170109
CitationJournal: Front Plant Sci / Year: 2023
Title: Receptor-like cytoplasmic kinase ScRIPK in sugarcane regulates disease resistance and drought tolerance in Arabidopsis.
Authors: Fang, J. / Chai, Z. / Huang, R. / Huang, C. / Ming, Z. / Chen, B. / Yao, W. / Zhang, M.
History
DepositionDec 9, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ScRIPK kinase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9483
Polymers36,4161
Non-polymers5312
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.170, 72.350, 79.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ScRIPK kinase protein


Mass: 36416.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharum hybrid cultivar (sugarcane) / Gene: NCGR_LOCUS634
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 40% v/v Polyethylene glycol 400, 0.19 mM Cymal-7, 10% v/v Polyethylene glycol 3350, 0.18 mM GDN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2021
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→32.06 Å / Num. obs: 23842 / % possible obs: 99.7 % / Redundancy: 12.79 % / CC1/2: 0.998 / Rmerge(I) obs: 0.138 / Χ2: 1.02 / Net I/σ(I): 13
Reflection shellResolution: 2.1→2.15 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 23842 / CC1/2: 0.853

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT4data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TOS

5tos


Resolution: 2.1→26.738 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 1947 8.38 %
Rwork0.2035 --
obs0.2059 23235 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→26.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 32 80 2326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072313
X-RAY DIFFRACTIONf_angle_d0.9623138
X-RAY DIFFRACTIONf_dihedral_angle_d11.6221359
X-RAY DIFFRACTIONf_chiral_restr0.053346
X-RAY DIFFRACTIONf_plane_restr0.005389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.15260.32171250.28161423X-RAY DIFFRACTION92
2.1526-2.21070.36521330.26561424X-RAY DIFFRACTION93
2.2107-2.27580.24821350.24171445X-RAY DIFFRACTION94
2.2758-2.34920.25571350.22741459X-RAY DIFFRACTION96
2.3492-2.43310.25151380.20641494X-RAY DIFFRACTION97
2.4331-2.53040.23581400.20071497X-RAY DIFFRACTION98
2.5304-2.64550.26331330.19861538X-RAY DIFFRACTION99
2.6455-2.78480.24951520.20881532X-RAY DIFFRACTION99
2.7848-2.95910.27161370.21151536X-RAY DIFFRACTION99
2.9591-3.18720.2491420.21961557X-RAY DIFFRACTION100
3.1872-3.50730.24861400.2091552X-RAY DIFFRACTION99
3.5073-4.01340.22381400.18791594X-RAY DIFFRACTION100
4.0134-5.05090.18631500.17431583X-RAY DIFFRACTION100
5.0509-26.730.22451470.20931654X-RAY DIFFRACTION98

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